Recurring Meeting of Cleveland Clinic Core Team

Date: June 30, 2015

Time: 10:30 AM EST

Means: In person meeting


  1. Ahmet Erdemir
  2. Snehal Chokhandre
  3. Robb Colbrunn
  4. Tara Bonner
  5. Omar Gad
  6. Connor Lough
  7. Diana Suciu
  8. Raghav Malik


  1. Discuss immediate action items from the last meeting.
  2. Mid-term presentations by research students.
  3. Decide immediate action items for the next meeting.
  4. Other.

Immediate Action Items:

Ongoing Action Items:


  1. Discuss immediate action items from the last meeting.
    • Ahmet disseminated the oks008 MR image sets and updated image segmentation specifications. In regard to image segmentation, there was a discussion on where to store files. Ahmet informed all that the segmentation files should be in the source code repository under specimen number which can hold subfolders for segmentation, geometry, mesh generation, etc. He advised the team to also refer to the wiki page on instructions for the source code repository. Ahmet anticipates that segmentations results will be separate files for each tissue and will be the raw tissue volume in NIFTI format and raw tissue surface in STL format. All these should be in a non-processed, e.g. not smoothed, form. He also reviewed specifications relevant to summer student projects. Snehal provided a sample patellofemoral joint kinematics/kinetics file for script development.
    • Craig went over convergence optimization workflow with the summer students. He still needs to provide sample MR images for oks008.
    • Snehal completed notes for the June 9, 2015 meeting. In order to test all tissue types at 20%/s, Snehal and Craig dissected a knee left over from a study conducted by Paul Saluan's team. They will use tissues from this knee to verify that the simplified tissue testing performs as expected. Snehal identified the camera to purchase for the optical measurement system, she will forward the website to Ahmet for purchasing.
    • Robb still needs to conduct post-experiment calibration of pressure sensor used for oks008 testing.
    • Connor segmented the registration markers for the first two knees. He has made corrections for patella registration to account for data from divot points probing to calculate transformations. He also seemed to implement a verification step comparing distances between markers as measured by Optotrak probing and by MRI. This needs to be incorporated in the script including its reporting. Robb wondered if Connor was comparing the sphere fit results to expected marker geometries. Currently, this is not done but can be implemented.
    • Diana completed the code to read and process contact pressure data. She needs to interact with Robb and Tara regarding the verification of her analysis, i.e., comparison of her results with the analysis of the .fsx file in Tekscan software.
    • Omar tried to implement normalization of RMS calculations, but abandoned it due to the fact that the range on some channels is 0 (such as mediolateral). Instead he will just provide min/max and RMS in engineering units. Robb noted that some artefacts in data may cause erroneous reduction of data, particularly when end-point of the time window of interest is used. An averaging of data within that time window or a data filtering approach to remove these signal artefacts can be employed.
    • Raghav worked on getting the SimpleCV work using Python. He has been having issues installing the library and he will figure out in the upcoming week. He also asked if image collection can be made to achieve a uniform contrast/color difference between tissue and background. Raghav and Snehal will look at ways to use different background colors or brightness and localization of lighting to improve contrast. Raghav also noted that the blue marks on sample tendon tissue causes measurement errors. Snehal noted that this can be resolved.
  2. Mid-term presentations by research students.
    • Omar gave a presentation on tibiofemoral joint mechanics data reduction and reproducibility analysis.
    • Diana gave a presentation on patellofemoral joint contact pressure processing and segmentation of tissues.
    • Connor gave a presentation on processing of registration marker data.
    • Raghav gave a presentation on his script for processing of images to acquire tissue thickness.
  3. Decide immediate action items for the next meeting.
    • See Immediate Action Items above.
  4. Other.
    • None noted.

RecurringMeetings/2015-06-30 (last edited 2016-05-04 22:09:50 by localhost)